Error using biomaRt
Entering edit mode
Last seen 5 months ago
United Kingdom

Hello everyone. I am trying to filter the protein-coding genes from a list using biomaRt, and I am getting an error. The weird thing is that I've used the same code chunk dozens of times without any problems. I'm using RStudio.

my code:

#Remove non conding
ensembl = useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
IDs= c(Tissue_Spec_Cleaned$Gene)
proteincode <- getBM(attributes=c("ensembl_gene_id","gene_biotype"),
                     filters = c("ensembl_gene_id","biotype"), 
                     values=list(IDs,"protein_coding"), mart=ensembl)
Error in `vctrs::vec_as_subscript()`:
! `...` must be empty.
x Problematic argument:
* call = call
Run `rlang::last_error()` to see where the error occurred.

Error in make_ansi_style(x[["color"]]) : 
  Unknown style specification: br_magenta

I've already tried reloading R and reinstalling the package, but I have no idea where this error is coming from

my session:

> sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

[1] LC_COLLATE=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252   
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C                      
[5] LC_TIME=Portuguese_Brazil.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] readxl_1.3.1   biomaRt_2.48.3

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7                  lattice_0.20-44             prettyunits_1.1.1          
 [4] png_0.1-7                   Rsamtools_2.8.0             Biostrings_2.60.2          
 [7] assertthat_0.2.1            digest_0.6.28               utf8_1.2.2                 
[10] BiocFileCache_2.0.0         cellranger_1.1.0            R6_2.5.1                   
[13] GenomeInfoDb_1.28.4         stats4_4.1.1                RSQLite_2.2.8              
[16] httr_1.4.4                  pillar_1.8.1                zlibbioc_1.38.0            
[19] rlang_1.0.6                 GenomicFeatures_1.44.2      progress_1.2.2             
[22] lazyeval_0.2.2              curl_4.3.2                  rstudioapi_0.13            
[25] blob_1.2.2                  S4Vectors_0.30.0            Matrix_1.5-2               
[28] BiocParallel_1.26.2         stringr_1.4.1               ProtGenerics_1.24.0        
[31] RCurl_1.98-1.4              bit_4.0.4                   DelayedArray_0.18.0        
[34] compiler_4.1.1              rtracklayer_1.52.1          pkgconfig_2.0.3            
[37] BiocGenerics_0.38.0         tidyselect_1.2.0            KEGGREST_1.32.0            
[40] SummarizedExperiment_1.22.0 tibble_3.1.4                GenomeInfoDbData_1.2.6     
[43] IRanges_2.26.0              matrixStats_0.62.0          XML_3.99-0.7               
[46] fansi_0.5.0                 withr_2.5.0                 crayon_1.5.2               
[49] dplyr_1.0.7                 dbplyr_2.1.1                rappdirs_0.3.3             
[52] GenomicAlignments_1.28.0    bitops_1.0-7                grid_4.1.1                 
[55] lifecycle_1.0.3             DBI_1.1.1                   AnnotationFilter_1.16.0    
[58] magrittr_2.0.1              cli_3.0.1                   stringi_1.7.5              
[61] cachem_1.0.6                XVector_0.32.0              xml2_1.3.2                 
[64] filelock_1.0.2              ellipsis_0.3.2              vctrs_0.3.8                
[67] generics_0.1.3              rjson_0.2.20                restfulr_0.0.13            
[70] ensembldb_2.16.4            tools_4.1.1                 bit64_4.0.5                
[73] Biobase_2.52.0              glue_1.6.2                  purrr_0.3.5                
[76] hms_1.1.1                   MatrixGenerics_1.4.3        parallel_4.1.1             
[79] fastmap_1.1.0               yaml_2.3.5                  AnnotationDbi_1.54.1       
[82] GenomicRanges_1.44.0        memoise_2.0.1               BiocIO_1.2.0
biomaRt • 1.5k views
Entering edit mode

Can you give an example of the values in IDs? I currently have no idea where and error from the vctrs package might be coming in, biomaRt doesn't use that package directly.

Entering edit mode

Here are the IDs:

> head(IDs)
[1] "ENSG00000243485" "ENSG00000237613" "ENSG00000268020" "ENSG00000240361" "ENSG00000186092"
[6] "ENSG00000238009"

I also have no idea what is going on

EDIT: I just reinstalled vctrs and the code worked again. I don't know why, but vctrs was giving some conflict. Thanks

Entering edit mode

Great! I guess vectrs is used in one of the packages further down the stack. I'm glad it's working again.


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